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Research

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Current research project

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Yeast strain design

As the bioinformatician at BioPhero, I am developing, implementing pipelines and analysing multi-omic data to contribute to developing new and better pheromone products. With the main aim to disrupt insect mating to control pests, isn’t it a genius and elegant solution? 

This new role allows me to follow my dreams of using my bioinformatics skills to solve pressing issues like climate change and food security. With my passion and experience, I will help to transition to a more sustainable future, where pheromones will be the main pest control method.

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Past research projects

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Palaeogenomics of Cinchona barks: On the chemical and genomic diversity of historical Fever tree barks

The fever tree (Rubiaceae: Cinchona spp.) has been widely used to treat malaria for hundreds of years due to the content of quinoline compounds that are stored in the bark. Originally from the Andes and known by indigenous peoples for its ameliorating effect on high recurrent fevers, the native Cinchona forests were heavily harvested and later on, plantations were established in other tropical countries. Despite the economic and pharmaceutical importance of the fever tree, taxonomic issues have prevented the elucidation of the evolutionary history of the Cinchona genus and its potential relation with its chemical diversity. 

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Furthermore, with the advent of palaeogenomics, it is now possible to obtain, analyse and authenticate DNA from historical samples, which often lack both vouchers and information about provenance. This PhD project uses historical Cinchona barks as a model of wood museomics aiming to provide new perspectives on the origin, application, and importance of the fever tree. In this thesis, it is shown that quinoline alkaloids in historical bark samples remain stable 150 years later, bringing museum specimens to life and casting new light on the chemical diversity and selection history of the fever tree. A first draft genome of Cinchona pubescens is presented, and it is suggested that genome skimming may provide more accurate phylogenetic resolution than a commercial global target capture kit. Finally, it is shown how genomic approaches can be used to trace samples of unknown provenance back to their origin.

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In silico identification of nsSNPs in resistance genes of three wild and cultivated Oryza varieties

Rice is the staple food for a large part of the human population in the world. Rice plants are threatened by pathogens. However, they have developed two defence mechanisms to resist pathogens. In this study, we focused on the resistant (R) proteins in different rice varieties that are encoded by NBS-LRR genes. It has been found that some motifs in the LRR domain are under strong positive selection in cultivated rice and other grass species. In this study, we aimed to determine if this feature was also present in wild rice varieties and to what extent. Material and Methods: The genome data of nine rice varieties were used as materials, including Oryza sativa japonica, Oryza sativa indica as cultivated rice and Oryza barthii, Oryza brachyantha, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctata and Oryza rufipogon as wild rice varieties. R gene identification was performed with BLAST searches and HMM approaches through PRGDB, then annotated with InterProScan, HMMPam and Pepcoil. Ortholog analysis was done by two approaches, phylogeny and sequences-based (Orthofinder).

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The phylogenetic analysis was performed through Fasttree using the CC-MHD region. Finally, a positive selection analysis was performed with PAML's yn00. Results: We identified the number of R genes ranging from 204 (O. meridionalis) to 551 (O. sativa indica). A common distribution trend of NBS-LRR encoding genes on chromosomes in all varieties was found; chromosomes 11 and 12 held from 26% to 40% of the total R gene amount. Additionally, we obtained 405 clades of ortholog R genes spanning the CC-MHD region in all varieties, suggesting a rapid conserved evolution and a window to improve resistance in cultivated varieties from wild ones. The results in the phylogenomic analysis confirmed previous results, showing that O. rufipogon and O. nivara are highly related to O. sativa cultivars. Oryza barthii was closely related to O. glumaepatula, while O. brachyantha was more divergent from the others. Selection pressure analyses in LRR domains among the R gene ortholog groups showed that an ortholog R gene group related to signal transduction was also found under positive selection (Ka/Ks=1.22). Additionally, its core region (xxLxLxx) was under strong positive selection (Ka/Ks=2.11), showing that R genes evolve rapidly not only in domesticated Oryza but also in wild varieties and might also be the key sites under selection in the process of rice domestication.

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Comparative genomics of two Pasteurella strains infecting bovine and alpacas.

Pneumonia is one of the main mortality causes in alpacas; and the second one in babies’ alpacas. It might be caused by several factors like bacteria, viruses, different host conditions or even a mixture of them. One of the factors mentioned is the microorganism Pasteurella multocida, which is also involved in Pasteurellosis of other domestic species, including alpacas. However, little is known about this infection, regardless of its importance. This thesis aims to compare the genomes of both strains infecting bovines and alpacas genomes, 36950 and UNMSM, respectively, to know the genomic structure of the strain isolated from alpacas and elicit which proteins are related to pathogenesis in both hosts.

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For that reason, we sequenced the genome of P. multocida affecting alpaca, performed structural and functional genomics analysis and then conducted comparative genomics analysis with P. multocida 36950. It was found that P. multocida strains UNMSM and 36950 share 1798 proteins, from which 121 were considered virulence factors. Additionally, although strain 36950 presents ICEPmu1¸ UNMSM strain does not. However, UNMSM has a unique 250 Kb region between six P. multocida multocida strains. Phylogenetic analysis showed that FUR protein is conserved between six P. multocida multocida strains. On the other hand, OMPH protein is variable between those strains. AtpD gene was also analysed, and we found that P. multocida UNMSM was highly variable among the other four subspecies’ atpD, which probably means that the UNMSM strain can be considered as a new subspecies.